The issue of drinking water quality compliance in small and medium scale water services is of paramount importance in relation to the 98/83/CE European Drinking Water Directive (DWD). Additionally, concerns are being expressed over the implementation of the DWD with respect to possible impacts on water quality from forecast changes in European climate with global warming and further anticipated reductions in north European acid emissions. Consequently, we have developed a decision support system (DSS) named ARTEM-WQ (AwaReness Tool for the Evaluation and Mitigation of drinking Water Quality issues resulting from environmental changes) to support decision making by small and medium plant operators and other water stakeholders. ARTEM-WQ is based on a sequential risk analysis approach that includes consideration of catchment characteristics, climatic conditions and treatment operations. It provides a holistic evaluation of the water system, while also assessing human health risks of organic contaminants potentially present in treated waters (steroids, pharmaceuticals, pesticides, bisphenol-a, polychlorobiphenyls, polycyclic aromatic hydrocarbons, petrochemical hydrocarbons and disinfection by-products; n = 109). Moreover, the system provides recommendations for improvement while supporting decision making in its widest context. The tool has been tested on various European catchments and shows a promising potential to inform water managers of risks and appropriate mitigative actions. Further improvements should include toxicological knowledge advancement, environmental background pollutant concentrations and the assessment of the impact of distribution systems on water quality variation.